Can taking rifampicin cause melanosis coli?

Possibly: Melanosis coli is a harmless brown discoloration of the inside of the colon. It is typically caused by laxative medications containing chemicals called "anthraquinones", which are also used to make dyes. Rifampin is not an anthraquinone, but it causes orange-colored urine, tears and stool. I assume it could cause a similar orange discoloration of the colon.

Med side effect: Doubtful. Melanosis coli is very common and can occur more frequently in females, those who use laxatives or who have inflammatory bowel disease. In general it can just happen so no need to try and see if a medication caused it. Speak to your md for more details if you are concerned but you may just "have it for no reason".